To reproduce:
1. Open QA attached project "NavMeshRepro.zip"
2. In Hierarchy window, select NavSurface Object and observe correctly baked mesh
3. In Project window, select Navigation FBX file and change it's Mesh Compression to Low or Medium (and Apply)
4. In Hierarchy window, select NavSurface object again
5. In Inspector window, click Bake and observe

Expected: NavMesh is baked with any compression quality selected
Actual: NavMesh is not baked on objects with Low or Medium Compression Quality (Off and High are baked as intended)

Reproduced in: 2018.3.14f1, 2018.4.0f1, 2019.1.2f1, 2019.2.0b2, 2019.3.0a2

Note1: NavMesh script not compatible with 2017.4.26f1 LTS, therefore, could not test
Note2; Standard baking via Navigation window works as intended